Chapter 3
Chemistry and molecular biology for the maker
The molecules of life, and the chemistry of what you build with
Human Biology for the Medical Maker
Why this chapter exists
- Materials are chemistry — what leaches out, and what disinfectant does to them
- Measurement is chemistry — glucose meters are enzyme electrodes
- The body defends its chemistry hard — narrow ranges mean small changes matter
The subset of chemistry that keeps recurring in device work — nothing more.
The bonds you will meet
| Bond | Strength | Where it matters to you |
|---|
| Covalent | Strong | The polymer backbone; breaking it is degradation |
| Ionic | Strong dry, weaker in water | Salts, electrolytes |
| Hydrogen bond | Weak alone, decisive together | Water; protein and DNA structure |
| Van der Waals | Very weak, scales with area | Fine-surface adhesion |
| Hydrophobic effect | Not a bond — collectively strong | Membranes self-assemble; proteins fold |
The hydrophobic effect is water pushing oily material out of its way — not oil attracting oil.
Water: one polar molecule, many consequences
| Property | Consequence |
|---|
| Excellent solvent for ions | Anything implanted sits in a wet, salty, conductive environment |
| High heat capacity | Body buffers temperature; water phantoms behave thermally like tissue |
| High latent heat | Sweating cools — and an occlusive enclosure defeats it |
| Surface tension | A press-fit seam wicks fluid and becomes a cleaning problem |
| Nearly incompressible | Tissue deforms by moving fluid — the origin of creep |
pH, and why the range is so narrow
- A log scale: one unit is a tenfold change
- Arterial blood: 7.35 to 7.45 — about a 25 percent span in hydrogen ions
- Outside roughly 6.8 to 7.8 is incompatible with life
- Gastric acid about 1.5 to 3.5; pancreatic secretion about 8
- Enzymes have pH optima; outside them, shape and function fall away
Buffers, breathing, and devices
The bicarbonate buffer
- CO₂ + H₂O ⇌ H₂CO₃ ⇌ H⁺ + HCO₃⁻
- Breathing adjusts pH in minutes; kidneys in hours to days
- Interpreting a blood gas is a clinical skill
Why pH matters to a device
- Enzyme sensors have a working pH range
- Polyesters hydrolyse and acidify themselves
- Implants sit in a warm, salty, variably acidic bath
- Drug formulation is largely a pH problem
The four classes of biological molecule
| Monomer | Polymer | Job in the body |
|---|
| Amino acid (20 kinds) | Protein | Enzymes, structure, transport, signalling, antibodies |
| Monosaccharide such as glucose | Polysaccharide | Energy store, structure, the cell-surface sugar coat |
| Fatty acid and glycerol | Lipid | Membranes, energy store, steroid hormones |
| Nucleotide: A, T or U, G, C | Nucleic acid | Information: DNA stores, RNA executes |
Proteins: shape determines function
- Primary: the amino acid sequence, set by the gene
- Secondary, tertiary, quaternary: folds held by weaker bonds
- Denaturation: losing the shape without breaking the sequence
- Caused by heat, pH, solvents — and adsorption onto a surface
- Collagen: a third of body protein; haemoglobin: four cooperating subunits
The most useful idea in biomaterials
Protein adsorption is the first thing that happens when any material meets blood or tissue.
Everything after — cell attachment, inflammation, clotting, encapsulation — responds to that layer.
Enzymes, and why every biosensor has a range
| Property | Why a device engineer cares |
|---|
| Specificity | Glucose oxidase responds to glucose and nothing else in blood |
| Temperature | Rate rises until the protein denatures; sensors have a shelf life |
| pH | Each enzyme has an optimum; buffering is part of the design |
| Saturation | Sets the upper end of a biosensor's linear range |
| Inhibition | Interference in a sensor; mechanism of many drugs |
Membranes, carbohydrates, and nucleic acids
The lipid bilayer
- Self-assembles by the hydrophobic effect
- A selective barrier, and fluid
- Electrically insulating: a capacitor with gated resistors
The others, briefly
- Glycocalyx: the sugar coat on cells and vessel linings
- DNA to RNA to protein
- PCR amplifies; sequencing reads
Bioenergetics: oxygen is the body's logistics problem
- Glycolysis: small ATP yield, no oxygen needed
- Mitochondria: large ATP yield, oxygen required
- Interrupt perfusion: ATP falls within minutes, pumps fail, cells swell
- Brain and heart muscle tolerate interruption poorly
- Basal metabolic rate: about 60 to 75 watts
Cell signalling and the language of pharmacology
| Term | Meaning |
|---|
| Agonist / antagonist | Binds and activates / binds and blocks a receptor |
| Pharmacokinetics | What the body does to the drug: absorption, distribution, metabolism, excretion |
| Pharmacodynamics | What the drug does to the body |
| Bioavailability | Fraction reaching the circulation; intravenous is 100 percent |
| Half-life | Time for concentration to halve; sets the dosing interval |
| Therapeutic index | Gap between effective and toxic dose |
Narrow therapeutic index — warfarin, lithium, digoxin — is why infusion pumps and dose software are safety-critical.
Engineering bridge: the chemistry you meet as a maker
Polymers, leachables, metals, textiles, glass, adhesion
Polymer chemistry, practically
| Concept | Why it bites |
|---|
| Thermoplastic or thermoset | Most thermoplastics deform in an autoclave; PEEK is an exception |
| Glass transition | PLA softens at about 55 to 65 degrees — a hot car or a dishwasher |
| Additives | The things most likely to leach; the datasheet may not name them |
| Hydrolysis and oxidation | Polyesters degrade with water; UV yellows and embrittles |
| Environmental stress cracking | Polycarbonate plus certain disinfectants cracks under stress |
| Processing history | The same polymer moulded, machined, or printed is three different parts |
| Elastomers | Silicone is the skin-contact workhorse; latex is a recognised allergen |
Extractables, leachables, and biocompatibility
- Extractables: what comes out under exaggerated conditions
- Leachables: what actually comes out in use
- Toxicological risk assessment: tolerable for this contact and duration?
- Biocompatibility is not a property of a material
- "Medical grade" feedstock establishes nothing about your finished part
Where leachables come from
| Source | Typical culprits |
|---|
| The polymer | Residual monomer, oligomers |
| Additives | Plasticisers, stabilisers, colourants |
| Processing | Mould release, lubricants, cutting fluids |
| Post-processing | Solvents, uncured resin, polishing compound |
| Textile finishes | Dyes, softeners, repellent and antimicrobial finishes |
| Sterilisation | Ethylene oxide residues; radiation by-products |
Workshop sensitisers: uncured resin, epoxy hardeners, isocyanates, rosin flux fume, nickel.
Metals, textiles, and glass
Metals and corrosion
- Passive oxide film protects stainless and titanium
- Crevices: corrosion and cleaning problem together
- Galvanic: mixing alloys is a design decision
- Nickel release: a common skin allergen
Textiles and glass
- Polyester tolerates hot laundering; elastane loses stretch
- Coated fabrics are uncleanable once breached
- Borosilicate tolerates thermal shock; soda-lime cracks
- Glass is inert but fails suddenly and sharply
Adhesion and surface chemistry
| Concept | Practical consequence |
|---|
| Surface energy | Metals and glass bond well; polypropylene, PTFE, silicone resist |
| Contact angle | A cheap proxy for surface energy and cleanability |
| Surface treatment | Plasma, corona, or flame raise surface energy — temporarily |
| Adhesive chemistry | Cyanoacrylate brittle; epoxy has a pot life; some silicones release acetic acid |
| Roughness | Better keying — and more protein adsorption and biofilm |
Clinical devices built on this chemistry
| Device | Chemistry |
|---|
| Glucose meter and CGM | Enzyme electrode; saturation sets the range; interstitial lag |
| Blood gas analyser | Ion-selective and gas electrodes |
| Haemodialysis | Diffusion and ultrafiltration across a membrane |
| Resorbable implants | Tuned hydrolysis of PLGA releasing a drug |
| Transdermal patch | Diffusion through a very good barrier |
| Wound dressings | Hydrocolloids, alginates, silver — moisture management |
| Glass vials | Type 1 borosilicate for low leaching |
Software and training
Software
- E-prescribing and dose calculators: safety-critical
- PyMOL, ChimeraX, Mol*: molecular visualisation
- AlphaFold: predicted protein structures
- RDKit, Avogadro: build and compute
Training and simulation
- Molecular model kits
- Virtual labs: Labster, LabXchange, PhET
- Medication administration and barcode trainers
- Demonstration apparatus: glassware plus sensors
Maker entry point: the physical molecular model
- Structures from the Protein Data Bank — free and open
- Printed surface for a whole folded protein
- Stacked laser-cut slices show internal cavities
- Bent-wire backbone; turned ball-and-stick kits
- State the resolution, what is omitted, and that colour is a convention
Worked example: why the handle got sticky
| Mechanism | Evidence | Check |
|---|
| Plasticiser migration | Tacky, slight dimensional change | Compare with a retained control sample |
| Hydrolysis | Brittle; worse when warm and humid | Mechanical comparison; storage humidity |
| UV oxidation | Yellowing, cracks on lit faces | Exposed face versus shaded face |
| Stress cracking | Cracks where stressed after cleaning | Which agent? Where are the cracks? |
| Cleaning residue | Tacky only; improves on rinsing | Rinse and re-examine |
Keep a control sample. Four of five mechanisms were predictable at design time.
Workshop exercise and exit criteria
- Build a phospholipid bilayer from clay or card
- Measure household pH; plot against the blood range
- Demonstrate a bicarbonate buffer with vinegar
- Make a molecule model, by a chosen method, with a limitations statement
- Start a retained control sample of a material you use
What this chapter does not establish
- You cannot assess biocompatibility — it is a specialist evaluation
- You cannot select or validate a sterilisation chemistry
- You cannot interpret a blood gas or glucose reading
- You have learned pharmacology vocabulary, not pharmacology
- A molecule model is a schematic — label it so
Next — Foundations of biology: life, cells, and how biologists work.